Because of its stem cell properties and numerous derivatives, the vertebrate neural crest (NC) represents an excellent system for examining questions of cell specification and differentiation during development. A gene regulatory network (GRN) defines the regulatory state of neural crest cells (Meulemans D & Bronner-Fraser M (2004) Dev Cell 7(3):291-299), such that modules of transcription factors function sequentially to first specify the neural plate border and then the nascent neural crest. The intricate regulatory interactions within the NC-GRN start with a group of transcription factors comprising an evolutionarily “inflexible” neural plate border regulatory unit, whose essential upstream function is to establish identity of the progenitor territory (Nikitina N, Sauka-Spengler T, & Bronner-Fraser M (2008) Proc Natl Acad Sci USA 105(51):20083-20088). Neural crest specifiers are genes responsible for formation of the neural crest. Sox10 is one of the earliest neural crest specifying genes, driving delamination and directly regulating numerous downstream effectors and differentiation gene batteries. FoxD3 is one of the first markers of pre-migratory neural crest in many vertebrate species including mouse, chick, Xenopus and zebrafish (Hromas et al., 1999; Kos et al., 2001; Labosky and Kaestner, 1998; Lister et al., 2006; Pohl and Knochel, 2001; Sasai et al., 2001; Yamagata and Noda, 1998). Identification of region-specific regulatory elements as described herein, provides an important tool for identifying and manipulating the spatially-specified neural crest cells.